Chuck & Sarah vs the CIA
by Chuckfan92
Summary: AU from 5.12, what if the accident with Ellie and Sarah returned Sarah's memories. Will Chuck and Sarah get the normal life the want so badly? First fanfic.
1. Chapter 1

**A/N First Fanfic, so please let me know how it is. Also I don't own Chuck.  
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><p>Sarah begins to wake up and realizes she is tired to a chair in a house. As she begins to focus and she sees Chuck sitting in front of her. <em>What is going on? <em>Sarah thinks to herself. _Did Chuck tie me up? And where exactly am I at? _She then notices that Chuck is about to say something.

"Hey. Look I know you don't remember me, I thought you'd remember this…" Chuck starts but Sarah cuts him off before he can continue

"What are you talking about of course I remember you, and is this house? And untie your wife before she gets even angrier!"

"Sarah, what is going on? Did you get the glasses from Agent Carmichael?"

"Quinn? Chuck what the hell is going on? Quinn is asking for Intersect glasses"

"Sarah, Quinn wiped your memory and told you that I was a traitor and sent you to get the intersect glasses."

"Chuck I'm so sorry for the things I've done but untie and get this damn ear piece out of my ear"

Chuck quickly unties Sarah and removes the ear piece Chuck tells Sarah that he's gonna call Casey and let him know that her memories are back. While Chuck is talking to Casey she begins to think about what she possibly could've done while working for Quinn _Did I kill anybody? Did I hurt Chuck? And my head is killing me… maybe that's how I got my memories back the head injury caused them to return._

"Casey! It's Chuck, Sarah got her memories back we're leaving now call of the hit."

"No can do Bartowski, they are already on their way and it seems that Quinn is in your house. Take Walker, deal with Quinn and go off grid." Casey replies

"All right, how long do we need to be hidden for?" Asks Chuck

"A few weeks, maybe more just until things calm down."

Chuck then returns to find Sarah standing in the same spot lost in thought. _I am so glad that I have MY Sarah back_ he thinks, then shakes his head to refocus himself.

"Sarah, Quinn is in the house. We need to take him out and then get out of here as soon as possible!"

"Um okay let's head downstairs and we'll find Quinn and knock him out and leave him for Casey to-"

"Ahhh Agent Walker, it seems you have your memories back." Quinn says "And I was so close to getting you to give me the intersect glasses but I guess I'll kill you both and take the intersect glasses any-"

Quinn drops to the ground with a tranq dart sticking out his chest

"I'll get you for this Agent Carmichael…" Then he passes out.

Sarah quickly rushes back to grab the rope that once had her tied up and orders Chuck to put Quinn in the chair.

"Sarah we need to leave now the calvary is on their way to arrest you and Quinn."

"Okay, but once we are on our way you are going to tell me what happened because the last thing I remember was being on the bullet train and you were making an intersect blocker." Sarah replies as they are already out the door and inside the nerd herder.

"Chuck go north, I have a safe house about eight hours from here in Lincoln."

"All right but I think we should find a motel to stay at once we get a new car and get a few hours away from Burbank." Says Chuck

"Like the motel we stayed at in Barstow?" Sarah says while wiggling her eye brows. "But this time might have a different outcome than the last one." She finishes with a big smile on her face, the one that is reserved just for Chuck.

That's when Chuck knows for sure that his Sarah is back and the car accident didn't have any damage. _That's it! It was the car accident that got Sarah's memories back._

"So you must be wondering why you woke up unconscious?" Chuck asks after a few minutes of comfortable silence.

"Yeah, it crossed my mind and also why my head is throbbing!" Sarah says "And you better have a good explanation and I want you to start from the bullet train."

"Okay so, after you knocked Quinn off the train he somehow got back on and you went after him by yourself and he trapped you on the last car and took you to a warehouse, where I'm assuming he blocked your memories, you activated your tracking device and we were able to get to where you were but by the time we got there Quinn had already moved you. Then a couple days later you showed up at our place all bloody and beaten saying you had killed Quinn and had to walk all the way back. I could tell something was off but I wasn't sure what. Then we went to the intersect room and you downloaded the intersect into the glasses but I was able to grab them as we you leaving. Then you blew up the intersect room with me, Casey, and Morgan still inside. You figured out that I had taken the glasses and held Ellie gun point to set up a trade, then I decided to have you and Ellie meet me somewhere else. Ellie pulled a crazy stunt realizing you weren't buckled and crashed into a parked car." Chuck takes a breath after finishing the story. Then he looks at Sarah and sees tears in her eyes.

"Sarah, baby what's wrong?"

"I could've killed you, my husband, and Ellie, I held her at gun point! Chuck, gun point! What do you think is wrong? I hated the way I was when I first met you and I am so sorry you had to see that person but I'm me now so we can finally quit the spy life and have a real family." Sarah said thru her tears.

"Yes we can but first we should find a place to stay for the night and also ditch this car."

After finding a car that seemed like nobody would miss Sarah followed Chuck to an abandoned road where he ditched the nerd herder and hoped in the car with Sarah. A little while later they pulled into a motel in Los Banos where they would stay for the night. They entered the motel room and quickly got ready for bed, they kissed each other good night and Sarah put her head on Chuck's chest while he wrapped her in his arms.

"Good night Chuck, I love you so much" Sarah said looking into Chuck's eyes.

"I love you too Sarah, good night" Chuck then kissed her forehead and they both drifted off to sleep.

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><p><strong>So how was that? Good? Bad? Let me know by reviewing please :)<strong>


	2. Chapter 2

**A/N: Wow! Thanks for all the reviews guys it means alot :) I realized in the summary that I said 5.11 and that was vs the Bullet Train so I fixed that and changed it to 5.12 where that car crash actually happend lol.  
>Also I don't own Chuck.<br>**

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><p>Director of the CIA John Kimble walked into his office and sat down at his desk to think about the situation he is in right now. <em>I've got two ex-spies on the run who ruined my plans of getting the intersect for myself<em> then he had a wicked thought. He picked up the phone and dialed a number that could get him removed as director of the CIA.

"Yes, I want you to remove two prisoners from the high security prison" Was the first thing he said when the person on the other line picked up.

"You don't have to tell me who to remove; I already know these two will help me get my revenge on Agent Walker." The female voice replied "I want Chuck Bartowski for myself."

"Good but it's not Walker anymore it's Bartowski, they got married last year" responded Kimble.

"Dammit, it's going to be even more difficult to get Chuck to fall in love with me again."

"Don't worry you will get Chuck Bartowski and get your Agent status reinstated when this is done Jill" said Kimble.

"Thank you sir, I'm not gonna fail you." Replied Jill Roberts.

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><p>Casey finishes his talk with Beckman about how the new CIA director might be a traitor and how he and Grimes needs to find Walker and Bartowski before he does.<p>

"Grimes any new hits about where Walker and Bartowski might be going?"

"Uh we caught the nerd herder going to an abandon road then 20 minutes later a black SUV take the same road as the nerd herder. Could be Sarah following Chuck to pick him up?" asked Morgan.

"Good idea try to track the license plate and see if we can get anywhere."

"Yes sir!" '

Casey just growled in annoyance and walked away. About ten minutes later Morgan cheered in success as he found the SUV and had Casey come and take a look.

"They stopped at a hotel in Los Banos that's only a few hours away. We can make it there before they wake up."

Casey looked at the clock and saw it was 5 in the morning and they had been working non stop since arresting Quinn at the house.

"All right Grimes lets go you can sleep on the way and I'll drive." Casey as they were leaving Castle.

"What? But I want to help and I don't need sleep I had three monsters while searching for Chuck and Sarah!"

"All the more reason to tranq you" Casey growled at him.

"Wha? Ahh Casey I thought you loved me?" Morgan started to slur and eventually passed out.

"Ahh sweet silence." Casey said to himself.

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><p>Chuck woke up the next morning to hear the shower running and figured that there would be no repeat performance of Barstow. <em>At least there's no Casey here to arrest us<em> and as soon as Chuck finished his thought the door burst open and in walked Casey and Morgan.

"Casey you are not bringing in me or Sarah we are heading to a safe house north of here-" Casey cut him off

"We aren't going to arrest you moron, the new CIA director is a traitor and Quinn never made it to the prison."

Sarah then chose to walk out of the bathroom only wrapped in a towel not looking where she was walking "Chuck go ahead and take a shower, I'm gonna go get us breakfast before we leave." Then she looked up and saw Morgan and Casey standing there.

"Sorry Casey but I won't let you bring us in, I'm so close to the live I want with Chuck and the CIA already tried to take it from us and I won't let the NSA do the same."

"Relax Walker we won't take you in, Beckman said that the new CIA director is a traitor and Quinn never made it to the prison."

"Whose the new director?"

"Uh John Kimble" said Morgan while giggling

"Was he a detective at one point?" Asked Chuck.

"No, why?" said Casey

"I'm Detective John Kimble!" Said Chuck in his best Austrian accent.

Morgan busted up laughing with Chuck while Sarah and Casey both looked really confused.

"Is that from a movie Chuck?" Asked Sarah, slightly amused by how hard Chuck and Morgan are laughing.

"Kindergarten Cop? Really? Arnold Schwarzenegger? Next movie night we are watching that all right?"

"I'm a Cop you idiot!" Said Morgan who's Arnold impersonation is a lot worse than Chuck's.

"Oh lord help us" Casey grumbled then his phone rang and stepped out of the room to answer the call.

"Who said you could have my cookies?"

"Uhh Morgan wrong movie, I think that's from Jingle All the Way" said Chuck.

"Stop whining!"

"That's better" replied Chuck, eventually Sarah got annoyed and realized she was still in a towel and left to go change into clothes. When Sarah returned Morgan looked right at her and said

"Who is your daddy and what does he do!" Morgan seemed to be on a roll but Casey returned and shot Morgan with a tranq dart.

"We've got a problem" said Casey.

"What's going on big guy?" asked Chuck.

"That was Beckman she said someone broke into the high security prison and broke out a certain prisoner. She also used the help of Quinn to break out the person." Casey said trying to avoid letting them know who broke in and who got broken out.

"She?" questioned Sarah.

"Jill Roberts."

"What? Jill Roberts? As in my ex girlfriend from Stanford turned Fulcrum agent? That Jill Roberts?" asked Chuck, he was starting to freak out.

Casey nodded "And it gets worse"

"How can that get worse Casey?"

"The person she and Quinn broke out was Shaw." Casey said

The room was silent from shock by what Casey just told them, except Morgan's loud snoring.

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><p><strong>AN: So what'd you think? I hope you don't hate me for bringing Shaw back but I think he was seriously the best bad guy Chuck has left.  
>Please review and let me know if it was good or bad.<strong>


	3. Chapter 3

**A/N: Sorry about the wait, I've got school and it's starting to pick up. Anyway here is the third chapter enjoy.**

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><p>Two weeks later… Lincoln, CA<p>

Chuck woke up feeling refreshed and knew that if he and Sarah weren't on the run, then this would be a pretty good morning. But after hearing from Casey that the terrible three (Morgan's nickname for Shaw, Quinn, and Jill) were spotted near Chicago and had Casey go and get the Awesome's and bring them to their safe house.

"Good morning O' husband of mine" Sarah said while walking into the room with a big smile on her face.

"Good morning beautiful" Chuck responded "Ellie, Clara, and Awesome are supposed to arrive with Casey in a few hours." Chuck notices that Sarah's happy mood vanishes quickly and is replaced with sadness and fear? _I'm pretty sure I can read Sarah's face by now and that is definitely fear_ he thinks to himself.

"Hey, what's wrong?" Chuck asks her.

"From what you said the last time I saw Ellie I held her at gunpoint and threatened to kill her" she says sadly "What if she hates me Chuck? I don't want you to lose your relationship with your sister because of me."

Chuck wraps his arms around her as he says "She won't hate you Sarah; she knows that wasn't the Sarah she has known for the last five years. And even if she does then she is going to have to live with the fact that you are my wife and I am never letting you go."

"Thank you Chuck" She replies with a smile that is growing bigger by the second.

"I mean it Sarah, I almost lost you for good this time and I am never letting you go again." Chuck responds seriously.

"Okay Chuck, I believe you. Now what do you say we go and make breakfast before the Awesomes arrive."  
>"Sounds like a wonderful plan to me." Chuck says then giving her a passionate kiss before heading to the kitchen.<p>

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><p>Casey pulls his Crown Victoria up in front of Chuck and Sarah's house and sees that's it has a white picket fence with a red door and Casey grunts with annoyance <em>typical Walker, trying to be a real girl<em>.

Ellie hears Casey's grunt and sees the Bartowski's house "Oh Chuck you would pick a house like the one in Burbank."

"Bartowski didn't pick this house, Walker did." Casey grunts in reply.

"Wow I didn't realize that CIA assassins didn't want to live in a house out of the fifties John." Ellie says in more of statement than a question. _I just hope that she didn't harm my brother in any way, or else I'm gonna end her. CIA spy or not._

"They are not supposed to but your brother somehow convinced Walker that mixing peanut butter and chocolate was a good idea then Walker was gone from there." Casey grunted in disgust thinking back at how many times he saw them kissing and talking about lady feelings. "Now get out of my car you three I have to be in Burbank to make sure Grimes doesn't do anything stupid."

"Fine, and thank you for the ride and taking us away from our house so we can live with a woman who wanted to kill me!" Ellie says angrily and grabs Clara and gets out of the car.

Devon being quiet the whole time finally decides to speak "Thanks for the ride John and I'm sorry about Ellie she's having a rough time with everything that happened with Sarah."

"Don't worry about it. But to be honest she was a little scarier than Walker when she yells at me."

Devon chuckles and gets out of the car to catch up with his wife but she had already rang the doorbell and the door opened to reveal Sarah. Then what happened next shocked him, Ellie then slapped Sarah as hard as she could and it literally knocked Sarah back too stunned to say anything. Ellie proceeded inside. He runs up to see if Sarah is okay but by the time he gets there Chuck already has her in his arms trying to stop the blonde from crying.

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><p>"Mmmm, Chuck that was such a good breakfast, your chocolate chip pancakes are amazing!" Sarah says finishing up her the last of her pancakes.<p>

"Why thank you! It was a rather good breakfast wasn't it? So what would you like to do before they get here?" Chuck asks giving her the Bartowski eyebrow dance.

Sarah giggles and gives him a kiss that shows him what she wants to do but she can't put into words what. Their make-out session is interrupted by the doorbell.

Sarah groans and tells Chuck that she will get the door. She gets up and opens the door and smiles "Hey Ellie how was-"

Ellie cuts her off by raising her hand and slapping Sarah as hard as she can "Bitch!" Sarah stumbles back not expecting to get slapped to see Ellie walk by her and into the kitchen. She collapeses to her knees and begins sobbing she fells two arms pull her into a hug.

"Shhh it's okay Sarah try to relax, she doesn't hate you she's just angry right now." Chuck says trying desperately to calm his wife down.

"No it's not okay she hates me and to be honest Chuck I don't blame her." Sarah says the sobbing never slowing down. Chuck finally looks up to see Devon and tells him he is going to put Sarah in bed and he will be down in a few minutes to talk about what happened.

_Uh oh, he did not look too happy. Ellie I really hope it felt good to do that because Chuck is very angry_ Devon thinks to himself as he joins Ellie in the kitchen.

"Ahh that felt soooo good to do that Devon, that CIA whore has been playing Chuck this whole time and I won't let her ruin our family anymore." Ellie says then looks at Devon and sees a not so happy expression on his face "What's wrong?"

"Ellie, you crossed a line back there and she didn't deserve that from-" Devon stops as he sees Chuck walking towards the kitchen "I uh will just go and eat Clara I mean feed Clara haha" Devon mumbles nervously and makes a quick exit from the room.

"Ellie what the hell is the matter with you?" Chuck says angrily looking at his sister.

"That that bitch held me at gun point and you expect me to forgive her just like that?"

"Ellie she got her memories back, she's MY Sarah now, that was Sarah from before we even knew her." Chuck tries to reason with Ellie.

"Exactly! How do you know that she's just playing you, that it's been just a cover for the last three years or whenever you actually got together?" Ellie says "She is a spy she is supposed to seduce you into what she wants." Ellie says as if she knew what the spy world was.

"It's not a cover Ellie! I don't know any other way to convince you but if you think you are just going to stand there and talk about how my WIFE is a bitch and a CIA whore or slut, then think again because right now you are not acting like my sister." Chuck finishes and leaves the room to go and be with his wife. _How dare she treat Sarah that way! Sarah thought of her as a sister and this is the way she treats her? I should be embarrassed that I even call her my sister._

"Sarah? Baby you okay?" Chuck asks entering their room.

"No." She says the sobbing has stopped but she is still sniffling "I heard the entire conversation I was halfway down the stairs when I heard you two talking. Chuck I am so so sorry for ruining your relationship with your sister."

"Sarah none of this was your fault, I'm thinking she's had these insecurities about you when she found out the truth about us being spies."

"Chuck can you just hold me? I feel so lonely right now and I need to feel your arms around me." Sarah says.

"Of course." Chuck says while getting in the bed behind Sarah and pulling her close.

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><p>"Dammit we were too late. They are already gone!" Shaw says furiously.<p>

"Shaw cool your jets, this is where Chuck's sister lives, they weren't gonna be here any way." Jill says _jeez I think I made a mistake in getting this guy out. No personality and he has anger issues._

"Yeah cool it Shaw getting angry won't get us anywhere." Quinn says

"Why are you even here Quinn?" Jill asks "I mean I want Chuck and Shaw wants Sarah dead for killing his wife. What type of revenge are you looking for?"

"Well I was supposed to get the intersect but now I just want a cheeseburger." Quinn says both Shaw and Jill exchanged confused looks "I mean it's been like 3 years since I've had a decent cheeseburger and not one from McDonalds those are just fake I want one from In n Out Burger when we get back to California and I also-" Quinn stops seeing there is a tranq dart sticking out of his chest "Really? I hate you so much Shaw." He is able to finish before he passes out.

"Good thing we shut him up. He reminds me of Morgan Grimes. Always talking and being really annoying." Jill says and Shaw just agrees with her.

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><p><strong>AN: I always felt that Ellie didn't have a strong enough reaction when she found out that Sarah was a spy and this is how I thought it should've played out.  
>The next chapter should have some action in it. I'll try to update soon so please review :)<strong>


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